file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 38.00 40.00 41.00 41.38 43.00 44.00
## [1] 40
## [1] 38 39 39 39 39 39 40 40 40 40 40 40 40 40 41 41 41 41 41 41 41 42 42 42 42
## [26] 42 43 43 43 43 43 43 43 43 43 43 43 44 44 44
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261
##
## FALSE TRUE <NA>
## 21 1718 261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 76 0.002350 99.8100
## 2: gene 1 0.000025 99.9975
## total_counts
## 1: 94
## 2: 1
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 94.48 99.58 93.53 99.97 100.00
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: AATK AATK AATK ENSG00000181409 FALSE
## 2: ABAT ABAT ABAT ENSG00000183044 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 3157 0.091525
## 2: NCBITaxon:9606 gene 9074 0.368950
## pct_dropout_by_counts total_counts selected
## 1: 92.1075 3661 1
## 2: 77.3150 14758 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "SIGLEC1" "CRYM" "RIPOR2" "GLT1D1" "ADGRA3"
## [6] "PID1" "ADAMTS3" "PAPSS2" "GOLGA8B" "HDAC4-AS1"
## [11] "MEIKIN" "RP11-120A1.1" "TRG-AS1" "IGSF9B" "LILRB5"
## [16] "ARFGEF3" "ADAM23" "MXI1" "PATJ" "PAM"
## [21] "ST18" "ZFYVE28" "JAML" "PLPP3" "CAMK2N1"
## [26] "SNED1" "ARHGEF3" "RANBP3L" "STXBP6" "TBC1D10C"
## [31] "MCTP1" "SRRM3" "TMTC2" "ADGRB1" "FAM153CP"
## [36] "AC093843.1" "SATB1-AS1" "DIRC3" "TRHDE-AS1" "LINC01322"
## [41] "SELENOP" "LINC01138" "RP11-335E8.3"
## [1] 2
## [1] "SLC4A7" "ZNF532" "TXNDC16" "POLA1" "VWA8"
## [6] "APBA1" "TENT5A" "SGK1" "DTD1" "RTN4IP1"
## [11] "LANCL2" "ERMN" "ADAMTS17" "FOXO1" "PUS10"
## [16] "SMIM14" "SOCS6" "PRDX6-AS1" "ZNF433-AS1" "RP13-188A5.1"
## [21] "TWIST2" "LINC01278" "ADAP1" "KLHL24" "FAM117B"
## [26] "CCNG2" "PELI2" "AUH" "PDK1" "AGPAT5"
## [31] "ETS2" "MARCHF8" "INSR" "CEBPB" "KCNE1"
## [36] "IFNLR1" "PLCG2" "CEBPD"
## [1] 3
## [1] "ABCB4" "TTC7A" "SYNDIG1" "CPED1"
## [5] "FAM149A" "TMEM156" "PEBP4" "GAREM1"
## [9] "ARL5C" "RASGEF1C" "TENM4" "TMEM163"
## [13] "DEPTOR" "GHRL" "LIPC" "MICOS10"
## [17] "MARCHF3" "C5orf64" "KBTBD12" "TSBP1-AS1"
## [21] "ZRANB2-AS2" "FSIP2-AS1" "RP11-634B7.4" "LINC01141"
## [25] "LINC01684" "KCNMB2-AS1" "LINC02008" "XACT"
## [29] "CTB-161M19.4" "LINC02232" "LINC01094" "RP11-541P9.3"
## [33] "RP11-946L16.1" "RP11-493L12.4" "RP11-399K21.11" "CH17-55D9.1"
## [37] "RP11-685G11.1" "NCMAP" "GLDN" "CCDC73"
## [41] "MYO16-AS1" "RP11-707P17.1" "RP11-452F19.4"
## [1] 4
## [1] "CEACAM1" "PLAGL1"
## [3] "RAB38" "SPATA6"
## [5] "ARMH4" "NKD1"
## [7] "DISP1" "DENND2B"
## [9] "ATF7IP2" "DLEU1"
## [11] "CATSPERE" "SPATA13_ENSG00000182957"
## [13] "SCFD2" "PRKN"
## [15] "MBD5" "AC007879.5"
## [17] "FTCDNL1" "AC105760.2"
## [19] "LINC01515" "MIR646HG"
## [21] "AC002539.1" "RPL34-DT"
## [23] "COX10-AS1" "RNF217-AS1"
## [25] "LINC01258" "RP11-130F10.1"
## [27] "LINC02762" "RHOXF1-AS1"
## [29] "RP11-323I15.5" "LINC00907"
## [31] "RP11-323P17.2" "CCDC28A-AS1"
## [33] "LINC01374" "EIF1B-AS1"
## [35] "RP11-692P14.1" "RP4-545L17.11"
## [37] "RP11-314E10.1" "RNASET2"
## [39] "ARHGAP6" "PILRA"
## [41] "GRK3" "BICRAL"
## [43] "PADI2"
## [1] 5
## [1] "MTHFS" "BRIP1" "SCAI" "ZNRF1" "RANBP17" "JARID2"
## [7] "NSMAF" "MSR1" "BCAT1" "ZFAT" "HACE1" "TBC1D2"
## [13] "INTS6" "DOT1L" "ARRDC2" "UBE2R2" "PPARD" "GBE1"
## [19] "PAPOLG" "RLF" "ESYT2" "ELL2" "TRIP10" "PHF21A"
## [25] "GLUL" "GFOD1" "MCPH1" "RIT2" "ASAP1" "CFDP1"
## [31] "CDCP1" "PPIP5K1" "AFF1" "KLHL6" "CHST15" "GPRIN3"
## [37] "RALGAPA2" "COL27A1" "ZNF277" "RGL3"
## [1] 6
## [1] "ARHGEF18" "ACYP2"
## [3] "RP11-131L23.1" "SLC16A1-AS1"
## [5] "XIST" "HMGA1P4"
## [7] "PVT1" "ATP6V0D1-DT"
## [9] "STAB1" "FAM50A"
## [11] "AK1" "GTDC1"
## [13] "KIAA0513" "TIAM2"
## [15] "SLC2A13" "PARP8"
## [17] "CFAP161" "ST3GAL2"
## [19] "TNFRSF11B" "GREM1"
## [21] "CXXC5" "LPCAT4"
## [23] "POTEG" "ZNF407"
## [25] "AC023469.1" "SNHG14"
## [27] "RP5-864K19.4" "ARL17B"
## [29] "CYP1B1-AS1" "LINC01762"
## [31] "RP11-154D17.1" "LINC01609"
## [33] "CTB-41I6.2" "MTRNR2L12"
## [35] "RMRP_ENSG00000269900" "SCARNA2_ENSG00000270066"
## [37] "LL22NC03-2H8.5" "RP11-154H23.4"
## [39] "CH507-513H4.1" "CH507-528H12.1"
## [41] "RP11-596C23.6" "RP11-344F5.1"
## [43] "AC003099.2"
## [1] 7
## [1] "NEXMIF" "ANGPT2" "LIPG" "NIPAL2"
## [5] "PLAT" "ECM2" "PODXL2" "NEK11"
## [9] "AKAP7" "PLAU" "OMD" "SGCE"
## [13] "FMO5" "PDE5A" "RAB40B" "MLIP"
## [17] "IRAK1BP1" "MMS22L" "RNF180" "MAMDC2"
## [21] "TMEM52B" "BEAN1" "B3GLCT" "COL5A2"
## [25] "MAMDC2-AS1" "LTC4S" "ENTPD3-AS1" "AC092431.3"
## [29] "RP11-123B3.2" "AC006160.5" "MRPS30-DT" "LIX1-AS1"
## [33] "PRANCR" "LINC02316" "RP11-305E17.8" "RP11-6G22.1"
## [37] "FSTL4" "SERPINE1" "GALNT18" "ARSK"
## [41] "SH3BGRL2" "ARHGEF25"
## [1] 8
## [1] "MUSK" "MMP24" "IER3" "CH25H"
## [5] "DPYS" "BEX3" "H2AC20" "SPDYE2"
## [9] "ANKUB1" "MTCP1" "DOCK4-AS1" "AC023590.1"
## [13] "ARHGAP26-AS1" "ZNF451-AS1" "RP11-165F24.3" "AC017101.10"
## [17] "ALG13-AS1" "AC083884.8" "RP1-117O3.2" "KCNMA1-AS1"
## [21] "BCL2L1-AS1" "RP11-544A12.4" "DENND6A-AS1" "RP5-1101C3.1"
## [25] "LINC00996" "RP11-39E3.3" "RP11-1H15.2" "RP11-434H14.1"
## [29] "RP1-71H24.1" "CTD-2647E9.3" "RP11-317G6.1" "RP11-106M3.3"
## [33] "RNF213-AS1" "PRKCA-AS1" "RP11-737O24.2" "RP11-16C1.3"
## [37] "TCF4-AS1" "H2AC19" "RP11-386I14.4" "RP11-1H15.4"
## [41] "AC009505.4" "CTD-2285E13.1"
## [1] 9
## [1] "DERA" "TYMP" "NME3" "PLGRKT"
## [5] "ENOSF1" "IFI44L" "HERC6" "FHAD1"
## [9] "ENPP3" "HESX1" "ZDHHC19" "FAM227B"
## [13] "OLR1" "ODF3B" "MCMDC2" "H2BC4"
## [17] "MX2" "TMSB4X" "RP11-115J16.1" "OVCH1-AS1"
## [21] "LINC02073" "H2BC8" "H2AC8" "H2BC7"
## [25] "RP1-111C20.3" "SLC2A3" "RGS1" "TGFB2"
## [29] "ITGB8" "SRGN" "RNF144B" "TMEM140"
## [33] "FRRS1" "TAMALIN" "ALDH1A1" "APLF"
## [37] "H1-0" "AF064858.6" "AC093818.1" "PIK3IP1-DT"
## [41] "IFITM10" "RP11-13N12.1"
## [1] 10
## [1] "ALDOC" "BEX2" "TET1" "FBN2"
## [5] "BCL2A1" "TNFRSF21" "AIM2" "MOBP"
## [9] "ABAT" "NFIX" "CD9" "PLEKHH3"
## [13] "ANO8" "PGM1" "PFKFB4" "USP9Y"
## [17] "KDM5B" "NR4A3" "HIF3A" "KDM6B"
## [21] "HILPDA" "MYO1G" "ADCY3" "LYPD5"
## [25] "CCDC107" "G6PD" "FBXO27" "ANKZF1"
## [29] "OTUD1" "FRMD5" "ADCY5" "TRNAU1AP"
## [33] "TNFAIP8L3" "TBKBP1" "TSPAN4" "STARD10"
## [37] "SLC12A8" "LUCAT1" "RP11-661A12.5"
## [1] 11
## [1] "MBNL3" "P3H2" "PIGL" "PUDP"
## [5] "GIPC2" "GPAT3" "IRF8" "ARHGAP42"
## [9] "ADAMTS15" "DNAJC24" "TLN2" "GAP43"
## [13] "ZMAT3" "PNMA3" "CDIN1" "SDHAF3"
## [17] "FIRRE" "ALOX12-AS1" "RP11-535M15.1" "AC073115.7"
## [21] "RP5-1198O20.4" "C12orf75" "LINC00894" "RP11-195C7.1"
## [25] "AC073115.6" "LINC00968" "RP11-679C8.2" "MIR3142HG"
## [29] "MIR222HG" "RP11-323F24.5" "RP11-111G13.1" "RGCC"
## [33] "SLC25A37" "SLC26A7" "DHRS3" "TLR5"
## [37] "LINC02397" "GCC2-AS1" "AC025171.1" "MYOCOS"
## [41] "RP11-249L21.6"
## [1] 12
## [1] "PDE10A" "IGSF11" "TMEM44" "BEND6"
## [5] "LINC00476" "FIGN" "ZNF804B" "DOK6"
## [9] "RP11-673E1.1" "PSMD7-DT" "RP11-640F22.1" "LINC02885"
## [13] "RP11-320L2.1" "ADGRL1" "COL5A3" "CDH20"
## [17] "DNAH6" "CHD5" "CSMD2" "PXDNL"
## [21] "PALM2AKAP2" "ANKRD30BL" "PRICKLE2" "ADGRV1"
## [25] "AMER2" "PDZRN4" "FSTL5" "GPC5"
## [29] "SSTR2" "SLIT1" "CR1L" "RORB"
## [33] "LINC00970" "BASP1-AS1" "RP11-191L9.4" "RP11-147G16.1"
## [37] "RP11-696N14.1" "RP11-17A1.3" "RP11-259O2.1" "LINC01414"
## [41] "CTC-535M15.2" "RP11-436D23.1" "LINC00551"
## [1] 13
## [1] "RP4-809F18.1" "MRC1" "SYT7" "PCDH11Y"
## [5] "FGF14" "ATP8A1" "ATP8A2" "ZNF365"
## [9] "RBMS3" "STXBP5L" "TENM2" "CNTN5"
## [13] "ADGRL3" "ZNF385D" "SPOCK1" "NCAM2"
## [17] "CLSTN2" "GABRB1" "CSMD3" "LRFN5"
## [21] "SEMA3E" "FUT9" "LRRC3B" "KCTD16"
## [25] "FLRT2" "PTPRT" "TAFA2" "ZNF521"
## [29] "LINC00632" "MIAT" "LINC01320" "LINC01435"
## [33] "SHISA9" "RP11-384F7.2" "SLC5A4-AS1" "CPEB2-DT"
## [37] "RP11-79E3.2" "RP11-20D14.3" "LINC00558" "U91319.1"
## [41] "IQCJ-SCHIP1" "RP4-799O8.1" "RP11-398J12.1"
## [1] 14
## [1] "BCAS3" "NUBPL" "B2M" "FTH1"
## [5] "XKR6" "RTTN" "ARSJ" "ZFP36L1"
## [9] "RPL41" "SLC1A3" "IRAK3" "SLC26A3"
## [13] "ANKRD12" "PRKAG2" "RAPGEF1" "CTSD"
## [17] "HS3ST2" "PTPRE" "SOX5" "CPM"
## [21] "SSH2" "SDK1" "ARID5B" "MERTK"
## [25] "FMNL2" "CDC42SE2" "CLASP2" "OXR1"
## [29] "ABCA1" "MTSS1" "BNC2" "CHD2"
## [33] "BAIAP2" "OPCML" "AS3MT" "AC013463.2"
## [37] "NEAT1" "RP11-368L12.1" "RP5-1015P16.1" "RENO1"
## [1] 15
## [1] "LDAH" "TEX9" "MTHFD2L" "TAGAP" "KIF5C-AS1"
## [6] "MTRNR2L8" "MYO9A" "CERS4" "MAP3K20" "CEP170B"
## [11] "KATNAL1" "STN1" "SNX25" "SEM1" "AFDN"
## [16] "DNAJB2" "DRAM1" "PGGHG" "NR6A1" "RSU1"
## [21] "LRRC4C" "CLEC1A" "BTBD11" "AMN1" "PITPNC1"
## [26] "FBXO32" "NEK10" "KLF13" "RESF1" "ZHX2"
## [31] "PARVB" "CTD-3088G3.8" "IARS1" "TOX" "LINC00862"
## [36] "ZDBF2" "C17orf67" "SGO1-AS1" "RP11-305L7.3" "CLEC5A"
## [41] "C2orf27A"
## [1] 16
## [1] "IPCEF1" "RBL1" "ARSB" "IFT43"
## [5] "METTL25" "CGNL1" "TBC1D14" "FRMD6"
## [9] "ITGA9" "C11orf49" "LRRC8C" "RAB39A"
## [13] "RNLS" "RTN4RL1" "ERC2" "CENPP"
## [17] "LIN52" "RP11-736I24.5" "CELSR3" "CLEC16A"
## [21] "LCP2" "DOCK3" "E2F3" "FRMD4B"
## [25] "HELLS" "RASSF8" "PRAM1" "WNT2B"
## [29] "PPFIA2" "SH3RF1" "SAMD12" "SERTAD2"
## [33] "AIDA" "SYCP2" "ROR1-AS1" "AC092835.2"
## [37] "LINC02646" "FMN1" "HCG17" "RP11-114N19.3"
## [41] "RP11-404C6.6"
## [1] 17
## [1] "PKD2L2" "ATP8B1"
## [3] "PCSK1N" "CALY"
## [5] "MCTP2" "ADAMTS19"
## [7] "RAB37" "IRAG1-AS1"
## [9] "TMEM151B" "EYS"
## [11] "FSIP2" "CARNMT1-AS1"
## [13] "SMCR5" "AC105461.1"
## [15] "PCDH9-AS2" "LINC01277"
## [17] "RP3-525N10.2" "RP1-225E12.2"
## [19] "COA6-AS1" "ARHGAP15-AS1"
## [21] "LANCL1-AS1" "RMDN2-AS1"
## [23] "KDM4A-AS1" "LRIG2-DT"
## [25] "LINC01877" "RP11-544A12.8"
## [27] "ALG1L9P_ENSG00000248671" "CTD-2537O9.1"
## [29] "RP11-571M6.7" "RP11-66H6.3"
## [31] "LINC00621" "CTD-3149D2.4"
## [33] "RP4-769N13.7" "COPG2IT1"
## [35] "RP11-237N2.1" "RP11-65F13.4"
## [37] "RP11-685G9.5" "RP11-617F9.2"
## [39] "RP11-399K19.1" "RASGRP2"
## [41] "OLFM1" "H1-10"
## [43] "CCDC71L" "RP11-322M13.1"
## [1] 18
## [1] "SNCAIP" "TRPM3" "MPP2" "GNLY" "CHN1" "RALGPS1"
## [7] "MEIS1" "TRPC1" "SYCE2" "CNTN1" "NCDN" "CELF4"
## [13] "CPE" "GABRG2" "KCNH1" "CDH18" "CACNA1B" "CRIM1"
## [19] "ME3" "HOMER1" "SCN3A" "CACNA2D1" "PTPRN2" "FMN2"
## [25] "SYN2" "SPTBN4" "EDIL3" "GRM5" "ZFPM2" "CNTNAP2"
## [31] "PPM1E" "CDH4" "UNC5C" "TSHZ2" "PBX1" "SYN3"
## [37] "MYT1L" "GRM7" "MIB2"
## [1] 19
## [1] "PRKCQ" "SLC26A4" "NLRP1" "PRTFDC1" "DAAM1" "PEX7" "WLS"
## [8] "DOCK10" "ZNF707" "HRH1" "HECW1" "SAMD4A" "PRKCH" "WWC3"
## [15] "LIMCH1" "RFX3" "RFX2" "DOCK9" "FNDC3A" "NHSL1" "SEMA6D"
## [22] "MAP3K6" "USP53" "DIXDC1" "EPB41" "STXBP5" "SLC43A2" "LDLRAD4"
## [29] "DHRSX" "CRADD" "TMEM51" "MALT1" "LRFN4" "PACS1" "SLC35E3"
## [36] "CARD11" "SLC48A1" "FADS3" "MICAL3"
## [1] 20
## [1] "OSBPL6" "GCNT2" "PARD3B" "RALGPS2" "MIS18BP1" "EPHB2"
## [7] "SLC22A23" "SMAD6" "STAMBPL1" "AIG1" "CD226" "MAGI1"
## [13] "PTPN14" "BACH1" "TIAM1" "PLEKHA7" "NXN" "S100Z"
## [19] "MBOAT1" "SH3RF3" "NCKAP5" "DNAH14" "TNFRSF1B" "PLEKHA5"
## [25] "RASSF2" "DENND1A" "SLC35E1" "ZBTB46" "STARD13" "AGAP3"
## [31] "DENND4C" "FNBP1L" "SLC2A5" "SRSF12" "AGAP1" "RBFOX3"
## [37] "FAM110B" "TANC2" "PELI1" "SIPA1L1"
## [1] 21
## [1] "PDK4" "TMSB10" "PER3" "SLC4A8" "DHRS9" "EFR3B"
## [7] "ITPR2" "NRN1" "ABCC4" "C3" "IL6ST" "LPAR6"
## [13] "PIGK" "KIF26B" "TMEM169" "P2RY12" "EMB" "CMKLR1"
## [19] "ATAD5" "CA8" "KIAA0825" "VKORC1L1" "LPAR1" "ATP9A"
## [25] "NEBL" "SLC16A10" "LIFR" "FAM162A" "SLC6A8" "KCNK1"
## [31] "TTYH3" "TMEM63B" "SLC12A6" "ATP8B2" "SSBP3" "SPRY1"
## [37] "GPRC5C" "PEAK1" "MAMDC4" "DGAT1"
## [1] 22
## [1] "HTR2B" "UBE2Q2" "ST3GAL1" "FAM107B"
## [5] "HDHD5" "PDE8A" "GRAMD4" "PPP1R15A"
## [9] "GALNT16" "RNF24" "RNMT" "BNIP3L"
## [13] "APBB3" "MGAT1" "CHI3L1" "BTG1"
## [17] "RGS16" "MYO10" "ARHGAP18" "PLIN2"
## [21] "HTR7" "ACSL1" "RASSF3" "CFAP251"
## [25] "RHOBTB3" "NFIL3" "DDIT4" "PPP1R3B"
## [29] "BNIP3" "FAM210A" "MITF" "CD55"
## [33] "ERO1A" "CD247" "LILRB3" "XKR9"
## [37] "ZSCAN31" "AF064858.8" "AC002066.1" "USP2-AS1"
## [41] "SBF2-AS1" "RP11-429A20.3"
## [1] 23
## [1] "ETV1" "OSBPL5" "MGLL" "RPH3A" "PITPNM2" "PDE4D" "PSD3"
## [8] "IER2" "CPLX1" "ATF5" "SKA2" "PKD1" "CDK14" "CDK17"
## [15] "PDE4A" "CTNNA2" "RAB27A" "FERMT2" "TNS1" "NPDC1" "SASH1"
## [22] "CCND3" "HPCAL1" "MOB3B" "IQSEC2" "DOCK6" "ZNF331" "SNAP25"
## [29] "IQSEC1" "NEK7" "SORCS3" "LRP1B" "ALOX15B" "ZDHHC20" "CADM1"
## [36] "PCDH9" "PDE4B" "RALYL" "OSBP2" "UNC13B"
## [1] 24
## [1] "ERCC8" "CECR2"
## [3] "SUSD1" "MAP2K6"
## [5] "CCDC18" "ITM2C"
## [7] "GAS2L3" "LRIG1"
## [9] "PLAC8" "SLC25A25"
## [11] "PSTPIP2" "CLIC2"
## [13] "UCN" "C1QA"
## [15] "PTPN2" "AATK"
## [17] "APOO" "LEKR1"
## [19] "LINC01605_ENSG00000253161" "RP11-154H12.3"
## [21] "RP4-681L3.3" "HGF"
## [23] "FNDC3B" "TRIP11"
## [25] "MTMR8" "TIMP1"
## [27] "MICU1" "TGFBI"
## [29] "KIF1A" "FCHO1"
## [31] "UBAP2" "DUSP10"
## [33] "GUK1" "PCNT"
## [35] "IL15" "CLIC4"
## [37] "GLRX" "GOLIM4"
## [39] "LIMK2" "SKIV2L"
## [41] "FMNL1-DT"
## [1] 25
## [1] "RPL3" "RPL18A" "RPL19" "RPL34" "RPL24" "IFIT3"
## [7] "IFIT2" "CCDC170" "ATP5F1E" "FGF13" "RPLP1" "RPS24"
## [13] "PRDM5" "RPS2" "RPS11" "RPL11" "SPAG16" "RPL32"
## [19] "FAU" "ATG10" "RPL26" "ELAVL4" "NFIA" "RPL38"
## [25] "RPLP2" "IFIT1" "RPS23" "CPNE4" "RPL12" "RPL23A"
## [31] "RPL39" "RORA-AS1" "MMP28" "SPOCK2" "SLC1A2" "CCNH"
## [37] "ZMAT4" "CMSS1" "ADARB1"
## [1] 26
## [1] "FOLR2" "C11orf65" "GLIPR1L1" "DLEU7"
## [5] "ENO4" "FAM177B" "LINC01285" "HNRNPA1P48"
## [9] "EDNRB-AS1" "LINC01375" "SLC8A1-AS1" "RP11-526K17.2"
## [13] "WEE2-AS1" "HCG22" "RP11-142M10.2" "SRGAP2-AS1"
## [17] "RNASEH2B-AS1" "RP11-353M9.1" "RP11-666F17.1" "RP11-142A5.1"
## [21] "RP11-712B9.2" "RP11-360F5.1" "CTD-2227I18.1" "RP11-238K6.1"
## [25] "RP11-624C23.1" "RP11-649G15.2" "RP11-463D19.1" "RP11-513G19.1"
## [29] "RP11-136F16.1" "RP11-370I10.2" "RP11-517O13.1" "LMO7-AS1"
## [33] "ABHD15-AS1" "RP11-354K4.2" "RP11-74J13.8" "CERNA2"
## [37] "RP1-80B9.4" "RP11-264E23.4" "RP11-7F3.1" "AC009166.9"
## [41] "RP11-56I23.2" "CTD-2021K4.2" "RP3-467L1.4"
## [1] 27
## [1] "ACER3" "EPDR1" "OGN" "MAP3K8" "SLC2A9"
## [6] "GALNT12" "FLVCR2" "SLC10A7" "SIRPD" "XAF1"
## [11] "EPSTI1" "PTH2R" "AOPEP" "LY96" "MAP3K7CL"
## [16] "RAB28" "TNFRSF13C" "PBX3" "WDR25" "PGBD5"
## [21] "PROS1" "MS4A4E" "LINC00630" "CCDC26" "CDKN2B-AS1"
## [26] "LINC02432" "C5orf17" "C8orf37-AS1" "LINC02328" "LINC01146"
## [31] "RP11-38B6.1" "RP13-52K8.2" "CDH26" "SEC14L1" "CHSY1"
## [36] "TLR2" "NGLY1" "CYRIA" "GK" "UBXN2B"
## [41] "MIR181A1HG"
## [1] 28
## [1] "IL7" "NEURL2" "LILRB2" "MIR4435-2HG"
## [5] "RP11-575L7.8" "CPB2-AS1" "STARD4-AS1" "ANK2-AS1"
## [9] "RP11-511B23.2" "RP11-638I2.8" "RP11-126O1.4" "RP11-793H13.14"
## [13] "RP11-622I12.1" "RP11-275G7.2" "RP11-261A24.1" "RP1-18C9.3"
## [17] "HIVEP2" "MAMLD1" "GADD45B" "IL4I1"
## [21] "TREM1" "CEMIP2" "GPNMB" "NIBAN2"
## [25] "RASGEF1B" "IER5" "VMO1" "ADSS1"
## [29] "ANKRD37" "ZNF395" "TPRG1" "LINC00910"
## [33] "H2BU1" "FAM229A" "LIMD1-AS1" "DARS1-AS1"
## [37] "RP11-47I22.3" "MIR155HG" "RP11-384C4.7" "LINC02698"
## [41] "HIF1A-AS3" "SAP30-DT" "RP11-475M20.2" "RP11-134L10.2"
## [1] 29
## [1] "LRRC6" "BEX1" "UNC80" "AC011288.2"
## [5] "LINC00923" "FAM66D" "CEROX1" "TENM1"
## [9] "LRRC7" "ZFY" "ARHGAP10" "TRHDE"
## [13] "SESN1" "RAPGEF4" "NALCN" "KCNT1"
## [17] "PCSK2" "EMILIN2" "PDZD2" "CBLN2"
## [21] "NPAS3" "AK5" "NLGN1" "CTNND2"
## [25] "NEGR1" "HPSE2" "CADM2" "RIMS2"
## [29] "RBM44" "NRXN1" "NELL2" "LSAMP"
## [33] "NRG3" "NPIPB15" "CACNA1E" "FAM155A"
## [37] "MEG3" "RP11-37N22.1" "AC067959.1" "RP11-657O9.1"
## [41] "CTC-340A15.2" "RMST" "RP11-111A21.1"
## [1] 30
## [1] "MCF2L2" "CARMIL1" "LRRC74A" "PROCR"
## [5] "CST3" "PLEK" "PIGC" "DUOX1"
## [9] "MED12L" "AGBL3" "C1QC" "BTG2"
## [13] "PAQR3" "SHOC1" "FILIP1L" "SLC35G2"
## [17] "DTWD2" "H2BC18" "AIF1" "RP11-321C24.1"
## [21] "ENTPD1-AS1" "RP4-568F9.6" "IPO9-AS1" "RP5-1132H15.1"
## [25] "LINC00960" "CTD-3239E11.2" "RP11-452H21.1" "RP11-867G2.8"
## [29] "CEACAM16-AS1" "KCNQ1OT1" "TSIX" "MIR223HG"
## [33] "LINC00624" "RP11-458A7.1" "RP11-13J12.3" "PDGFB"
## [37] "COL5A1" "DHRS13" "MFSD4B" "H2AC6"
## [41] "CTD-2643I7.5"
## [1] 31
## [1] "SP140" "AZIN2" "BANK1" "C4orf19"
## [5] "ADGRG5" "GASK1B" "PLD4" "TMC7"
## [9] "MIR31HG" "CYSLTR1" "PLCXD3" "CLEC9A"
## [13] "LINC01357" "LINC00539" "LINC02642" "LINC00884"
## [17] "RP11-120D5.1" "PTCHD4" "LINC02211" "MIR4300HG"
## [21] "GPRC5D-AS1" "LINC02057" "LINC01091" "AC008697.1"
## [25] "ZFPM2-AS1" "RP11-745L13.2" "CTC-575N7.1" "MAILR"
## [29] "RP11-10H3.1" "SMIM35" "RP11-630C16.2" "RP11-554D14.6"
## [33] "LINC02444" "RP11-588H23.3" "RP11-72M17.1" "RP11-187O7.3"
## [37] "LINC02712" "RP11-495L19.1" "RP11-437L7.2" "RP11-622O11.6"
## [41] "RP11-168F24.3" "RP1-236J16.3" "RP11-4F5.3"
## [1] 32
## [1] "TPD52" "ABCG2" "STON2" "RNF157" "MYO5B" "TSPYL2" "FGR"
## [8] "MATK" "TGFBR3" "ATP1B3" "MLF2" "IL27RA" "POU6F2" "HAVCR1"
## [15] "CYTIP" "EPHA4" "SLC2A1" "GNA13" "HSPH1" "ELK1" "SLC41A2"
## [22] "FGF2" "LARP1B" "GNA12" "SNTG1" "ADD3" "RNF144A" "RASGRP3"
## [29] "MSI2" "LONRF1" "MYO1E" "FGF17" "PTMS" "ZNF143" "PRKCB"
## [36] "LPL" "EFNA5" "SOGA3" "ITGB3"
## [1] 33
## [1] "CALCR" "IGF1" "PRDM11" "MTERF1"
## [5] "TMEM241" "NPL" "SLC49A4" "KCNMB1"
## [9] "LINC00467" "SAMSN1" "KCNMA1" "AUTS2"
## [13] "CX3CR1" "ZNF608" "MT1E" "GPR34"
## [17] "SPTLC3" "FGGY" "CAPS2" "RP11-445F6.2"
## [21] "TEX41" "RP11-162D16.2" "LINC00271" "RFX3-AS1"
## [25] "UFL1-AS1" "LINC01376" "BDNF-AS" "LINC01184"
## [29] "RP11-319G6.1" "RP11-381K20.2" "RP11-692D12.1" "ZNF10"
## [33] "RP11-370I10.6" "RP11-281A20.2" "RP11-19D22.1" "TMED8"
## [37] "DARS1" "OGFRL1" "ABCG1" "TMEM65"
## [41] "LONRF3" "ZC3H6"
## [1] 34
## [1] "ANGPTL1" "SLC5A9" "ADGRG2" "INSYN2B"
## [5] "AC002463.3" "ELMO1-AS1" "TMLHE-AS1" "AC096558.1"
## [9] "AC037445.1" "RP11-528G1.2" "MYCBP2-AS1" "DIAPH2-AS1"
## [13] "CCDC200" "AC018890.6" "RP11-775D22.3" "ZBTB20-AS5"
## [17] "MEF2C-AS2" "CTD-2015H6.3" "RHOQ-AS1" "RP11-268P4.5"
## [21] "RP11-506H20.1" "AP000487.6" "RP11-196H14.2" "RP11-493L12.3"
## [25] "RP11-713N11.4" "USP3-AS1" "RP11-815J21.4" "RP11-16B9.1"
## [29] "RP11-621L6.2" "RP11-703M24.5" "RP11-793A3.2" "RP11-58G13.1"
## [33] "RP11-53B2.3" "RP1-256G22.2" "CTD-2282P23.2" "RP11-121C2.3"
## [37] "LINC02666" "DISC2" "RP11-314L11.1" "GS1-98E2.1"
## [41] "RP11-21M24.6" "RP11-1146N6.3" "RP11-555K12.4" "NRG2"
## [1] 35
## [1] "PLPP1" "HAMP" "ADGRD1" "CYREN"
## [5] "SSPN" "ACKR4" "ARHGAP20" "WDPCP"
## [9] "SLC9B1" "TMEM144" "GPR85" "NLGN4Y"
## [13] "CYTL1" "B3GNT5" "TTTY14" "FLJ40194"
## [17] "PCED1B" "SCOC-AS1" "LINC02649" "AC003090.1"
## [21] "RP11-202G18.1" "AC007682.1" "RAP2C-AS1" "RP11-557H15.4"
## [25] "ITGA9-AS1" "FBXO30-DT" "RP11-246A10.1" "ARHGAP8"
## [29] "RP11-796E2.4" "FAM198B-AS1" "RP11-281P23.2" "LINC02742"
## [33] "RP11-37B2.1" "RP11-486A14.2" "RP11-516C1.1" "CTD-2336H13.2"
## [37] "LINC01572" "ZNF528-AS1" "RP11-419I17.1" "RP11-574F11.4"
## [41] "RP6-91H8.6" "RP11-221G19.1" "RP11-321P16.3"
## [1] 36
## [1] "PFN2" "ABCC1" "ABCA5" "DENND5B" "GTF2IRD1" "VCAN"
## [7] "ABCA7" "KCNAB2" "CPSF1" "RAP1GAP" "ZNF586" "ITPKC"
## [13] "MYOM1" "NDFIP2" "FLT1" "DGKH" "HSF4" "CLIP4"
## [19] "TSHZ3" "ZC4H2" "HIP1" "SH3BP5" "RAMP1" "MACROD1"
## [25] "MICAL2" "GDF11" "PLXNC1" "CPNE8" "RPP38" "CAMK4"
## [31] "ACOT11" "GMEB1" "ATOH8" "FRMD3" "C11orf80" "JAKMIP2"
## [37] "ZBTB7A" "ZBTB7C" "SESTD1" "NHEJ1"
## [1] 37
## [1] "SCMH1" "ADAM28" "ST6GAL1" "CENPK"
## [5] "FOXP2" "PCBD2" "GARNL3" "GSTCD"
## [9] "EFCAB11" "FRMD4A" "ANO10" "ARHGAP25"
## [13] "NMNAT3" "SFMBT1" "PRMT9" "NAALADL2"
## [17] "SLC9A9" "DYNC2H1" "SRGAP3" "KCNMB2"
## [21] "SFMBT2" "CCDC7" "MEI4" "SCIN"
## [25] "ARHGAP15" "CTTNBP2" "LAPTM4B" "CLNK"
## [29] "FOXP1" "HPCAL4" "FAM13A" "CSGALNACT1"
## [33] "FER" "JAZF1" "ADK" "ROBO1"
## [37] "RNF150" "MSRA" "MAML2" "GDI1"
## [41] "RP11-351A11.1"
## [1] 38
## [1] "ICA1" "OPHN1" "CASS4" "GPATCH2"
## [5] "CD69" "IL1A" "RCAN3" "ZRANB3"
## [9] "IL1B" "NRGN" "TSPAN7" "CACNA1D"
## [13] "PLXDC1" "CCDC171" "MACROD2" "KCNIP1"
## [17] "CACNB4" "COL25A1" "LIPE-AS1" "STX18-AS1"
## [21] "MIR100HG" "RP11-160E2.6" "RP11-413N10.3" "ADAM22"
## [25] "NCS1" "NCOA7" "CLVS2" "CACNA1C"
## [29] "MAPK13" "DLGAP1" "KCND3" "DPP10"
## [33] "CSMD1" "KCND2" "ANKS1B" "PRKG1"
## [37] "KCNIP4" "MAGI2" "KAZN" "RYR2"
## [1] 39
## [1] "ZFP64" "NAV3" "APBB1IP" "TRIM2"
## [5] "PLCL1" "CFAP74" "GASK1A" "SESN3"
## [9] "SETBP1" "NAV2" "ZDHHC14" "TCERG1L"
## [13] "SLC8A1" "KCNQ3" "ATP6AP1L" "MIR99AHG"
## [17] "LINC01356" "TMEM72-AS1" "RP1-30E17.2" "CTA-292E10.6"
## [21] "LMCD1-AS1" "KIF9-AS1" "AC097721.2" "HDAC2-AS2"
## [25] "MEF2C-AS1" "GMDS-DT" "LINC01301" "LINC02055"
## [29] "LINC00506" "KCNQ2" "CUX2" "WDR45B"
## [33] "HTR1E" "FUT10" "KCNQ5" "ZNF846"
## [37] "LNCAROD" "KLF3-AS1" "RP1-179N16.6" "MTRNR2L1"
## [41] "RP11-81K2.1" "RP11-396B14.2" "RP11-358F13.1"
## [1] 40
## [1] "HHAT" "STS" "ZNF821" "GDAP1"
## [5] "MS4A4A" "ADGRG6" "F13A1" "ZSCAN5A"
## [9] "AHI1" "ABCA8" "CDYL2" "GLYATL1"
## [13] "GRIK1" "RFLNA" "LINC02884" "LINC02196"
## [17] "LINC00639" "DISC1FP1" "RP11-341N18.1" "RP11-120L14.1"
## [21] "GCLC" "GCLM" "ARAP2" "SLC9A7"
## [25] "MEGF9" "DCUN1D4" "GYPC" "RGL1"
## [29] "CAMKMT" "TNFAIP8" "THRB" "RASA2"
## [33] "STARD9" "GPHN" "SH3PXD2B" "ARL4C"
## [37] "DPYD" "EFCAB2" "DENND1B" "AGBL1"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_7"
## [1] "NEXMIF" "ANGPT2" "LIPG" "NIPAL2"
## [5] "PLAT" "ECM2" "PODXL2" "NEK11"
## [9] "AKAP7" "PLAU" "OMD" "SGCE"
## [13] "FMO5" "PDE5A" "RAB40B" "MLIP"
## [17] "IRAK1BP1" "MMS22L" "RNF180" "MAMDC2"
## [21] "TMEM52B" "BEAN1" "B3GLCT" "COL5A2"
## [25] "MAMDC2-AS1" "LTC4S" "ENTPD3-AS1" "AC092431.3"
## [29] "RP11-123B3.2" "AC006160.5" "MRPS30-DT" "LIX1-AS1"
## [33] "PRANCR" "LINC02316" "RP11-305E17.8" "RP11-6G22.1"
## [37] "FSTL4" "SERPINE1" "GALNT18" "ARSK"
## [41] "SH3BGRL2" "ARHGEF25"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 241 dissolution of fibrin clot 3.01944e-05 1
## numDEInCat numInCat FDR
## 241 3 3 0.03568978
##
## [1] "set_9"
## [1] "DERA" "TYMP" "NME3" "PLGRKT"
## [5] "ENOSF1" "IFI44L" "HERC6" "FHAD1"
## [9] "ENPP3" "HESX1" "ZDHHC19" "FAM227B"
## [13] "OLR1" "ODF3B" "MCMDC2" "H2BC4"
## [17] "MX2" "TMSB4X" "RP11-115J16.1" "OVCH1-AS1"
## [21] "LINC02073" "H2BC8" "H2AC8" "H2BC7"
## [25] "RP1-111C20.3" "SLC2A3" "RGS1" "TGFB2"
## [29] "ITGB8" "SRGN" "RNF144B" "TMEM140"
## [33] "FRRS1" "TAMALIN" "ALDH1A1" "APLF"
## [37] "H1-0" "AF064858.6" "AC093818.1" "PIK3IP1-DT"
## [41] "IFITM10" "RP11-13N12.1"
## $reactome
## category
## 244 dna damage telomere stress induced senescence
## 9 activated pkn1 stimulates transcription of ar androgen receptor regulated genes k
## 76 assembly of the orc complex at the origin of replication
## 89 base excision repair ap site formation
## 247 dna methylation
## 293 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## 453 inhibition of dna recombination at telomere
## 789 recognition and association of dna glycosylase with site containing an affected p
## 863 rho gtpases activate pkns
## 1016 sirt1 negatively regulates rrna expression
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 244 1.044623e-06 1.0000000 5 9
## 9 2.618321e-05 0.9999995 4 8
## 76 2.618321e-05 0.9999995 4 8
## 89 2.618321e-05 0.9999995 4 8
## 247 2.618321e-05 0.9999995 4 8
## 293 2.618321e-05 0.9999995 4 8
## 453 2.618321e-05 0.9999995 4 8
## 789 2.618321e-05 0.9999995 4 8
## 863 2.618321e-05 0.9999995 4 8
## 1016 2.618321e-05 0.9999995 4 8
## FDR
## 244 0.001234744
## 9 0.002634916
## 76 0.002634916
## 89 0.002634916
## 247 0.002634916
## 293 0.002634916
## 453 0.002634916
## 789 0.002634916
## 863 0.002634916
## 1016 0.002634916
##
## [1] "set_23"
## [1] "ETV1" "OSBPL5" "MGLL" "RPH3A" "PITPNM2" "PDE4D" "PSD3"
## [8] "IER2" "CPLX1" "ATF5" "SKA2" "PKD1" "CDK14" "CDK17"
## [15] "PDE4A" "CTNNA2" "RAB27A" "FERMT2" "TNS1" "NPDC1" "SASH1"
## [22] "CCND3" "HPCAL1" "MOB3B" "IQSEC2" "DOCK6" "ZNF331" "SNAP25"
## [29] "IQSEC1" "NEK7" "SORCS3" "LRP1B" "ALOX15B" "ZDHHC20" "CADM1"
## [36] "PCDH9" "PDE4B" "RALYL" "OSBP2" "UNC13B"
## $reactome
## category over_represented_pvalue
## 203 darpp 32 events 1.935443e-05
## 6 acetylcholine neurotransmitter release cycle 1.268236e-04
## 641 norepinephrine neurotransmitter release cycle 1.268236e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 203 1.0000000 3 3 0.02287693
## 6 0.9999986 3 5 0.04996849
## 641 0.9999986 3 5 0.04996849
##
## [1] "set_25"
## [1] "RPL3" "RPL18A" "RPL19" "RPL34" "RPL24" "IFIT3"
## [7] "IFIT2" "CCDC170" "ATP5F1E" "FGF13" "RPLP1" "RPS24"
## [13] "PRDM5" "RPS2" "RPS11" "RPL11" "SPAG16" "RPL32"
## [19] "FAU" "ATG10" "RPL26" "ELAVL4" "NFIA" "RPL38"
## [25] "RPLP2" "IFIT1" "RPS23" "CPNE4" "RPL12" "RPL23A"
## [31] "RPL39" "RORA-AS1" "MMP28" "SPOCK2" "SLC1A2" "CCNH"
## [37] "ZMAT4" "CMSS1" "ADARB1"
## $reactome
## category over_represented_pvalue
## 138 cellular response to starvation 0
## 301 eukaryotic translation elongation 0
## 302 eukaryotic translation initiation 0
## 452 influenza infection 0
## 557 metabolism of amino acids and derivatives 0
## 640 nonsense mediated decay nmd 0
## 801 regulation of expression of slits and robos 0
## 850 response of eif2ak4 gcn2 to amino acid deficiency 0
## 901 rrna processing 0
## 927 selenoamino acid metabolism 0
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 19 26 0
## 301 1 19 23 0
## 302 1 19 23 0
## 452 1 19 27 0
## 557 1 19 41 0
## 640 1 19 23 0
## 801 1 19 27 0
## 850 1 19 25 0
## 901 1 19 25 0
## 927 1 19 26 0
##
## $go_bp
## category over_represented_pvalue
## 630 cytoplasmic translation 0.000000e+00
## 4283 ribosome biogenesis 2.296954e-10
## 4279 ribosomal large subunit biogenesis 1.495557e-08
## 4278 ribosomal large subunit assembly 5.803312e-07
## 4281 ribosomal small subunit biogenesis 2.788234e-06
## 4282 ribosome assembly 2.822479e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 630 1 19 23 0.000000e+00
## 4283 1 8 13 5.420811e-07
## 4279 1 5 5 2.353010e-05
## 4278 1 4 4 6.847909e-04
## 4281 1 4 5 2.220350e-03
## 4282 1 4 5 2.220350e-03
##
## [1] "set_38"
## [1] "ICA1" "OPHN1" "CASS4" "GPATCH2"
## [5] "CD69" "IL1A" "RCAN3" "ZRANB3"
## [9] "IL1B" "NRGN" "TSPAN7" "CACNA1D"
## [13] "PLXDC1" "CCDC171" "MACROD2" "KCNIP1"
## [17] "CACNB4" "COL25A1" "LIPE-AS1" "STX18-AS1"
## [21] "MIR100HG" "RP11-160E2.6" "RP11-413N10.3" "ADAM22"
## [25] "NCS1" "NCOA7" "CLVS2" "CACNA1C"
## [29] "MAPK13" "DLGAP1" "KCND3" "DPP10"
## [33] "CSMD1" "KCND2" "ANKS1B" "PRKG1"
## [37] "KCNIP4" "MAGI2" "KAZN" "RYR2"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 113 cardiac conduction 1.656815e-06 0.9999999
## 599 muscle contraction 6.418779e-06 0.9999997
## numDEInCat numInCat FDR
## 113 6 18 0.001958355
## 599 6 24 0.003793499
##
## $go_bp
## category
## 3683 regulation of monoatomic ion transmembrane transport
## 22 action potential
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3683 1.055834e-05 0.9999989 9 64
## 22 1.401989e-05 0.9999993 6 24
## FDR
## 3683 0.03308693
## 22 0.03308693
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955046 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16667435 127.2 31295163 238.8 65536 31295163 238.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0